Starting phenix.real_space_refine on Tue Mar 3 14:39:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rt4_54245/03_2026/9rt4_54245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rt4_54245/03_2026/9rt4_54245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rt4_54245/03_2026/9rt4_54245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rt4_54245/03_2026/9rt4_54245.map" model { file = "/net/cci-nas-00/data/ceres_data/9rt4_54245/03_2026/9rt4_54245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rt4_54245/03_2026/9rt4_54245.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 1927 2.51 5 N 489 2.21 5 O 588 1.98 5 H 2976 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5992 Number of models: 1 Model: "" Number of chains: 2 Chain: "C1" Number of atoms: 4287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4287 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "N2" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1705 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 4 Time building chain proxies: 1.24, per 1000 atoms: 0.21 Number of scatterers: 5992 At special positions: 0 Unit cell: (65.871, 60.241, 86.139, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 588 8.00 N 489 7.00 C 1927 6.00 H 2976 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYSC1 6 " - pdb=" SG CYSC1 185 " distance=2.03 Simple disulfide: pdb=" SG CYSC1 197 " - pdb=" SG CYSC1 282 " distance=2.03 Simple disulfide: pdb=" SG CYSC1 222 " - pdb=" SG CYSC1 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 242.5 milliseconds 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 706 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 6 sheets defined 25.8% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'C1' and resid 19 through 23 removed outlier: 3.525A pdb=" N VALC1 22 " --> pdb=" O SERC1 19 " (cutoff:3.500A) Processing helix chain 'C1' and resid 25 through 39 Processing helix chain 'C1' and resid 65 through 78 removed outlier: 3.529A pdb=" N ARGC1 78 " --> pdb=" O GLUC1 74 " (cutoff:3.500A) Processing helix chain 'C1' and resid 86 through 102 removed outlier: 3.793A pdb=" N GLYC1 90 " --> pdb=" O TYRC1 86 " (cutoff:3.500A) Processing helix chain 'C1' and resid 103 through 106 Processing helix chain 'C1' and resid 121 through 136 Processing helix chain 'C1' and resid 149 through 157 Processing helix chain 'C1' and resid 159 through 161 No H-bonds generated for 'chain 'C1' and resid 159 through 161' Processing helix chain 'C1' and resid 169 through 175 removed outlier: 4.420A pdb=" N LYSC1 174 " --> pdb=" O GLNC1 171 " (cutoff:3.500A) Processing helix chain 'C1' and resid 176 through 185 Processing sheet with id=AA1, first strand: chain 'C1' and resid 56 through 63 removed outlier: 5.215A pdb=" N ILEC1 58 " --> pdb=" O VALC1 51 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VALC1 51 " --> pdb=" O ILEC1 58 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEUC1 62 " --> pdb=" O LEUC1 47 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEUC1 47 " --> pdb=" O LEUC1 62 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N PHEC1 164 " --> pdb=" O VALC1 140 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYSC1 142 " --> pdb=" O PHEC1 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C1' and resid 187 through 191 removed outlier: 7.052A pdb=" N SERC1 207 " --> pdb=" O LEUC1 189 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEUC1 191 " --> pdb=" O VALC1 205 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VALC1 205 " --> pdb=" O LEUC1 191 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SERC1 238 " --> pdb=" O LEUC1 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C1' and resid 195 through 197 removed outlier: 5.629A pdb=" N VALC1 196 " --> pdb=" O THRC1 280 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEUC1 275 " --> pdb=" O VALC1 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N2' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'N2' and resid 69 through 72 removed outlier: 7.156A pdb=" N TYRN2 246 " --> pdb=" O SERN2 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N2' and resid 87 through 92 140 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2975 1.03 - 1.22: 2 1.22 - 1.42: 1282 1.42 - 1.61: 1772 1.61 - 1.80: 17 Bond restraints: 6048 Sorted by residual: bond pdb=" N GLNC1 1 " pdb=" CA GLNC1 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" N GLNC1 1 " pdb=" H GLNC1 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" CG LEUN2 249 " pdb=" CD2 LEUN2 249 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.66e+00 bond pdb=" C TRPN2 254 " pdb=" N TYRN2 255 " ideal model delta sigma weight residual 1.332 1.317 0.015 1.40e-02 5.10e+03 1.19e+00 bond pdb=" CB ARGC1 209 " pdb=" CG ARGC1 209 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.16e+00 ... (remaining 6043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 10480 1.21 - 2.43: 393 2.43 - 3.64: 31 3.64 - 4.85: 9 4.85 - 6.07: 4 Bond angle restraints: 10917 Sorted by residual: angle pdb=" CA GLNC1 192 " pdb=" CB GLNC1 192 " pdb=" CG GLNC1 192 " ideal model delta sigma weight residual 114.10 108.25 5.85 2.00e+00 2.50e-01 8.55e+00 angle pdb=" N GLNC1 192 " pdb=" CA GLNC1 192 " pdb=" C GLNC1 192 " ideal model delta sigma weight residual 109.81 115.88 -6.07 2.21e+00 2.05e-01 7.53e+00 angle pdb=" C GLNC1 192 " pdb=" N PROC1 193 " pdb=" CA PROC1 193 " ideal model delta sigma weight residual 119.84 116.57 3.27 1.25e+00 6.40e-01 6.85e+00 angle pdb=" C LEUC1 189 " pdb=" N GLUC1 190 " pdb=" CA GLUC1 190 " ideal model delta sigma weight residual 122.10 117.94 4.16 1.66e+00 3.63e-01 6.28e+00 angle pdb=" N SERN2 83 " pdb=" CA SERN2 83 " pdb=" C SERN2 83 " ideal model delta sigma weight residual 113.88 110.91 2.97 1.23e+00 6.61e-01 5.85e+00 ... (remaining 10912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 2599 14.13 - 28.27: 162 28.27 - 42.40: 56 42.40 - 56.53: 26 56.53 - 70.67: 8 Dihedral angle restraints: 2851 sinusoidal: 1547 harmonic: 1304 Sorted by residual: dihedral pdb=" CB CYSC1 197 " pdb=" SG CYSC1 197 " pdb=" SG CYSC1 282 " pdb=" CB CYSC1 282 " ideal model delta sinusoidal sigma weight residual 93.00 123.97 -30.97 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA TYRN2 270 " pdb=" C TYRN2 270 " pdb=" N TYRN2 271 " pdb=" CA TYRN2 271 " ideal model delta harmonic sigma weight residual -180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 dihedral pdb=" CB CYSC1 222 " pdb=" SG CYSC1 222 " pdb=" SG CYSC1 246 " pdb=" CB CYSC1 246 " ideal model delta sinusoidal sigma weight residual -86.00 -60.81 -25.19 1 1.00e+01 1.00e-02 9.13e+00 ... (remaining 2848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 358 0.041 - 0.082: 69 0.082 - 0.124: 33 0.124 - 0.165: 8 0.165 - 0.206: 1 Chirality restraints: 469 Sorted by residual: chirality pdb=" CA GLNC1 192 " pdb=" N GLNC1 192 " pdb=" C GLNC1 192 " pdb=" CB GLNC1 192 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CG LEUC1 189 " pdb=" CB LEUC1 189 " pdb=" CD1 LEUC1 189 " pdb=" CD2 LEUC1 189 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA VALC1 226 " pdb=" N VALC1 226 " pdb=" C VALC1 226 " pdb=" CB VALC1 226 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 466 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPN2 254 " -0.024 2.00e-02 2.50e+03 1.37e-02 7.53e+00 pdb=" CG TRPN2 254 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRPN2 254 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRPN2 254 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRPN2 254 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRPN2 254 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRPN2 254 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRPN2 254 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRPN2 254 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRPN2 254 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRPN2 254 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRPN2 254 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRPN2 254 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRPN2 254 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRPN2 254 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRPN2 254 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGC1 209 " -0.121 9.50e-02 1.11e+02 4.09e-02 2.81e+00 pdb=" NE ARGC1 209 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARGC1 209 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARGC1 209 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARGC1 209 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARGC1 209 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARGC1 209 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARGC1 209 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARGC1 209 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRPN2 81 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.17e+00 pdb=" N PRON2 82 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRON2 82 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRON2 82 " -0.021 5.00e-02 4.00e+02 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 2497 2.37 - 2.93: 13602 2.93 - 3.49: 15316 3.49 - 4.04: 21311 4.04 - 4.60: 31103 Nonbonded interactions: 83829 Sorted by model distance: nonbonded pdb=" HD2 TYRC1 141 " pdb=" HE1 PHEC1 164 " model vdw 1.814 2.100 nonbonded pdb=" HG SERC1 179 " pdb=" HD1 TYRN2 289 " model vdw 1.888 2.100 nonbonded pdb=" HD2 ARGC1 78 " pdb="HH11 ARGC1 78 " model vdw 1.924 2.270 nonbonded pdb=" HD2 TYRN2 255 " pdb=" H LYSN2 256 " model vdw 1.926 2.100 nonbonded pdb=" HD3 ARGC1 155 " pdb="HH11 ARGC1 155 " model vdw 1.931 2.270 ... (remaining 83824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3075 Z= 0.221 Angle : 0.610 6.066 4161 Z= 0.334 Chirality : 0.045 0.206 469 Planarity : 0.005 0.055 526 Dihedral : 9.754 70.666 1116 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.42), residues: 375 helix: 0.72 (0.57), residues: 80 sheet: -0.14 (0.45), residues: 132 loop : -1.41 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGC1 209 TYR 0.013 0.002 TYRC1 30 PHE 0.007 0.001 PHEN2 220 TRP 0.046 0.003 TRPN2 254 HIS 0.002 0.001 HISC1 88 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3072) covalent geometry : angle 0.60796 ( 4155) SS BOND : bond 0.00288 ( 3) SS BOND : angle 1.32475 ( 6) hydrogen bonds : bond 0.18127 ( 140) hydrogen bonds : angle 7.52809 ( 381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C1 160 LYS cc_start: 0.8719 (ptmt) cc_final: 0.8432 (ptmm) REVERT: C1 161 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8381 (mt-10) REVERT: N2 38 LYS cc_start: 0.8592 (tttm) cc_final: 0.8209 (mttp) REVERT: N2 95 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7353 (ttpt) REVERT: N2 239 ILE cc_start: 0.8607 (mt) cc_final: 0.8337 (pt) REVERT: N2 253 GLU cc_start: 0.7823 (mm-30) cc_final: 0.6662 (pt0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 1.3899 time to fit residues: 114.9466 Evaluate side-chains 55 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N2 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.143115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115896 restraints weight = 12309.950| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.68 r_work: 0.3402 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3075 Z= 0.198 Angle : 0.575 5.497 4161 Z= 0.304 Chirality : 0.045 0.172 469 Planarity : 0.004 0.032 526 Dihedral : 4.122 14.561 412 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.90 % Allowed : 9.91 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.44), residues: 375 helix: 1.79 (0.63), residues: 81 sheet: -0.03 (0.43), residues: 136 loop : -1.46 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGC1 209 TYR 0.009 0.001 TYRC1 30 PHE 0.008 0.001 PHEC1 52 TRP 0.021 0.002 TRPN2 254 HIS 0.004 0.002 HISN2 283 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 3072) covalent geometry : angle 0.57485 ( 4155) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.77257 ( 6) hydrogen bonds : bond 0.04479 ( 140) hydrogen bonds : angle 5.57141 ( 381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: C1 160 LYS cc_start: 0.8547 (ptmt) cc_final: 0.8147 (ptmm) REVERT: C1 161 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8095 (mt-10) REVERT: C1 189 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8967 (mm) REVERT: N2 38 LYS cc_start: 0.8688 (tttm) cc_final: 0.7966 (mttp) REVERT: N2 88 ASN cc_start: 0.7599 (m110) cc_final: 0.7102 (m110) REVERT: N2 95 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7429 (ttpt) REVERT: N2 239 ILE cc_start: 0.8462 (mt) cc_final: 0.8113 (tt) REVERT: N2 248 ASP cc_start: 0.8702 (m-30) cc_final: 0.8489 (m-30) REVERT: N2 253 GLU cc_start: 0.7904 (mm-30) cc_final: 0.6705 (pt0) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 0.9279 time to fit residues: 59.2634 Evaluate side-chains 53 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 149 GLU Chi-restraints excluded: chain C1 residue 189 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N2 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.115831 restraints weight = 12193.267| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.70 r_work: 0.3433 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3075 Z= 0.149 Angle : 0.512 4.801 4161 Z= 0.270 Chirality : 0.043 0.157 469 Planarity : 0.003 0.024 526 Dihedral : 4.059 15.397 412 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.90 % Allowed : 12.01 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.44), residues: 375 helix: 2.09 (0.64), residues: 82 sheet: 0.13 (0.42), residues: 136 loop : -1.30 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGC1 78 TYR 0.010 0.001 TYRC1 30 PHE 0.007 0.001 PHEC1 170 TRP 0.015 0.001 TRPN2 254 HIS 0.002 0.001 HISC1 88 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3072) covalent geometry : angle 0.51174 ( 4155) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.54826 ( 6) hydrogen bonds : bond 0.03921 ( 140) hydrogen bonds : angle 5.16060 ( 381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.205 Fit side-chains REVERT: C1 160 LYS cc_start: 0.8526 (ptmt) cc_final: 0.8057 (ptmm) REVERT: N2 38 LYS cc_start: 0.8706 (tttm) cc_final: 0.8010 (mttp) REVERT: N2 88 ASN cc_start: 0.7640 (m110) cc_final: 0.7182 (m110) REVERT: N2 95 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7368 (tmmt) REVERT: N2 239 ILE cc_start: 0.8507 (mt) cc_final: 0.8204 (pt) REVERT: N2 253 GLU cc_start: 0.7871 (mm-30) cc_final: 0.6708 (pt0) outliers start: 3 outliers final: 1 residues processed: 58 average time/residue: 1.0388 time to fit residues: 62.0055 Evaluate side-chains 51 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N2 residue 86 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 183 GLN N2 86 ASN N2 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114370 restraints weight = 12348.831| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.72 r_work: 0.3389 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3075 Z= 0.169 Angle : 0.527 6.049 4161 Z= 0.279 Chirality : 0.043 0.157 469 Planarity : 0.003 0.023 526 Dihedral : 4.127 15.638 412 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.30 % Allowed : 12.61 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.44), residues: 375 helix: 2.12 (0.63), residues: 82 sheet: 0.25 (0.42), residues: 136 loop : -1.26 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGC1 78 TYR 0.008 0.001 TYRC1 30 PHE 0.006 0.001 PHEC1 52 TRP 0.014 0.001 TRPN2 254 HIS 0.002 0.001 HISN2 283 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 3072) covalent geometry : angle 0.52733 ( 4155) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.48657 ( 6) hydrogen bonds : bond 0.03704 ( 140) hydrogen bonds : angle 5.03742 ( 381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: C1 160 LYS cc_start: 0.8434 (ptmt) cc_final: 0.8052 (ptmm) REVERT: N2 38 LYS cc_start: 0.8719 (tttm) cc_final: 0.8005 (mttp) REVERT: N2 88 ASN cc_start: 0.7683 (m110) cc_final: 0.7058 (m110) REVERT: N2 95 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7384 (tmmt) REVERT: N2 239 ILE cc_start: 0.8495 (mt) cc_final: 0.8250 (pt) REVERT: N2 253 GLU cc_start: 0.7899 (mm-30) cc_final: 0.6720 (pt0) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 1.0491 time to fit residues: 59.3312 Evaluate side-chains 49 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 2 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 162 GLN N2 86 ASN N2 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.141766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114851 restraints weight = 12546.723| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.74 r_work: 0.3398 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3075 Z= 0.122 Angle : 0.491 5.148 4161 Z= 0.258 Chirality : 0.043 0.156 469 Planarity : 0.003 0.024 526 Dihedral : 4.082 16.455 412 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.20 % Allowed : 12.01 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.44), residues: 375 helix: 2.17 (0.62), residues: 82 sheet: 0.25 (0.43), residues: 136 loop : -1.30 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGC1 78 TYR 0.008 0.001 TYRC1 30 PHE 0.006 0.001 PHEC1 52 TRP 0.011 0.001 TRPN2 254 HIS 0.002 0.001 HISN2 283 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3072) covalent geometry : angle 0.49148 ( 4155) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.39048 ( 6) hydrogen bonds : bond 0.03427 ( 140) hydrogen bonds : angle 4.86741 ( 381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: C1 160 LYS cc_start: 0.8428 (ptmt) cc_final: 0.8035 (ptmm) REVERT: N2 38 LYS cc_start: 0.8692 (tttm) cc_final: 0.7968 (mttp) REVERT: N2 88 ASN cc_start: 0.7588 (m110) cc_final: 0.7059 (m110) REVERT: N2 95 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7372 (tmmt) REVERT: N2 239 ILE cc_start: 0.8508 (mt) cc_final: 0.8222 (pt) REVERT: N2 253 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6656 (pt0) outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 1.0091 time to fit residues: 59.1365 Evaluate side-chains 51 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 207 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N2 86 ASN N2 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113814 restraints weight = 12330.551| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.70 r_work: 0.3385 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3075 Z= 0.144 Angle : 0.491 4.665 4161 Z= 0.259 Chirality : 0.043 0.154 469 Planarity : 0.003 0.028 526 Dihedral : 4.064 16.165 412 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.20 % Allowed : 12.61 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.45), residues: 375 helix: 2.27 (0.62), residues: 82 sheet: 0.02 (0.41), residues: 155 loop : -1.51 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGC1 78 TYR 0.009 0.001 TYRC1 30 PHE 0.006 0.001 PHEC1 170 TRP 0.011 0.001 TRPN2 254 HIS 0.002 0.001 HISC1 88 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3072) covalent geometry : angle 0.49145 ( 4155) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.41492 ( 6) hydrogen bonds : bond 0.03471 ( 140) hydrogen bonds : angle 4.80514 ( 381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: C1 160 LYS cc_start: 0.8404 (ptmt) cc_final: 0.8121 (ptmm) REVERT: N2 38 LYS cc_start: 0.8718 (tttm) cc_final: 0.8007 (mttp) REVERT: N2 88 ASN cc_start: 0.7589 (m110) cc_final: 0.7074 (m110) REVERT: N2 95 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7376 (tmmt) REVERT: N2 239 ILE cc_start: 0.8542 (mt) cc_final: 0.8208 (pt) REVERT: N2 253 GLU cc_start: 0.7835 (mm-30) cc_final: 0.6677 (pt0) outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 1.0284 time to fit residues: 57.1657 Evaluate side-chains 53 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 207 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 183 GLN N2 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112408 restraints weight = 12294.771| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.72 r_work: 0.3380 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3075 Z= 0.171 Angle : 0.501 4.702 4161 Z= 0.263 Chirality : 0.043 0.155 469 Planarity : 0.003 0.028 526 Dihedral : 4.130 16.439 412 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.90 % Allowed : 12.61 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.45), residues: 375 helix: 2.22 (0.62), residues: 82 sheet: -0.03 (0.41), residues: 155 loop : -1.49 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGC1 78 TYR 0.010 0.001 TYRC1 30 PHE 0.006 0.001 PHEC1 40 TRP 0.013 0.001 TRPN2 254 HIS 0.002 0.001 HISC1 88 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3072) covalent geometry : angle 0.50069 ( 4155) SS BOND : bond 0.00234 ( 3) SS BOND : angle 0.49584 ( 6) hydrogen bonds : bond 0.03522 ( 140) hydrogen bonds : angle 4.81325 ( 381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.197 Fit side-chains REVERT: C1 160 LYS cc_start: 0.8403 (ptmt) cc_final: 0.8121 (ptmm) REVERT: N2 38 LYS cc_start: 0.8740 (tttm) cc_final: 0.7989 (mttp) REVERT: N2 95 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7371 (tmmt) REVERT: N2 239 ILE cc_start: 0.8589 (mt) cc_final: 0.8199 (pt) REVERT: N2 253 GLU cc_start: 0.7891 (mm-30) cc_final: 0.6748 (pt0) outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 1.0213 time to fit residues: 56.8185 Evaluate side-chains 51 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 207 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N2 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113289 restraints weight = 12229.827| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.70 r_work: 0.3387 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3075 Z= 0.175 Angle : 0.502 4.594 4161 Z= 0.266 Chirality : 0.043 0.156 469 Planarity : 0.004 0.047 526 Dihedral : 4.181 16.598 412 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.50 % Allowed : 12.01 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.45), residues: 375 helix: 2.24 (0.62), residues: 82 sheet: -0.05 (0.41), residues: 155 loop : -1.52 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGC1 78 TYR 0.012 0.001 TYRC1 30 PHE 0.006 0.001 PHEC1 40 TRP 0.012 0.001 TRPN2 254 HIS 0.002 0.001 HISC1 88 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3072) covalent geometry : angle 0.50238 ( 4155) SS BOND : bond 0.00249 ( 3) SS BOND : angle 0.51381 ( 6) hydrogen bonds : bond 0.03517 ( 140) hydrogen bonds : angle 4.81141 ( 381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: C1 160 LYS cc_start: 0.8309 (ptmt) cc_final: 0.8017 (ptmm) REVERT: N2 38 LYS cc_start: 0.8768 (tttm) cc_final: 0.8002 (mttp) REVERT: N2 95 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7392 (tmmt) REVERT: N2 253 GLU cc_start: 0.7895 (mm-30) cc_final: 0.6725 (pt0) outliers start: 5 outliers final: 1 residues processed: 51 average time/residue: 1.0538 time to fit residues: 55.3818 Evaluate side-chains 50 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 207 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N2 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114632 restraints weight = 12216.874| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.72 r_work: 0.3410 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3075 Z= 0.133 Angle : 0.485 4.582 4161 Z= 0.254 Chirality : 0.043 0.155 469 Planarity : 0.004 0.040 526 Dihedral : 4.111 17.050 412 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.60 % Allowed : 13.51 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.45), residues: 375 helix: 2.25 (0.61), residues: 82 sheet: 0.03 (0.41), residues: 155 loop : -1.48 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGC1 78 TYR 0.010 0.001 TYRC1 30 PHE 0.005 0.001 PHEC1 52 TRP 0.009 0.001 TRPN2 254 HIS 0.002 0.001 HISC1 88 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3072) covalent geometry : angle 0.48502 ( 4155) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.49703 ( 6) hydrogen bonds : bond 0.03353 ( 140) hydrogen bonds : angle 4.75181 ( 381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: C1 160 LYS cc_start: 0.8265 (ptmt) cc_final: 0.7969 (ptmm) REVERT: N2 38 LYS cc_start: 0.8747 (tttm) cc_final: 0.7982 (mttp) REVERT: N2 95 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7389 (tmmt) REVERT: N2 253 GLU cc_start: 0.7846 (mm-30) cc_final: 0.6693 (pt0) outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.9698 time to fit residues: 49.0076 Evaluate side-chains 48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 207 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 24 ASN N2 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113853 restraints weight = 12250.094| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.72 r_work: 0.3393 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3075 Z= 0.152 Angle : 0.491 4.631 4161 Z= 0.259 Chirality : 0.043 0.155 469 Planarity : 0.004 0.038 526 Dihedral : 4.126 16.807 412 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.90 % Allowed : 12.91 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.45), residues: 375 helix: 2.26 (0.61), residues: 82 sheet: 0.03 (0.41), residues: 155 loop : -1.51 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGC1 78 TYR 0.011 0.001 TYRC1 125 PHE 0.005 0.001 PHEC1 52 TRP 0.011 0.001 TRPN2 254 HIS 0.002 0.001 HISC1 88 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3072) covalent geometry : angle 0.49086 ( 4155) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.51821 ( 6) hydrogen bonds : bond 0.03402 ( 140) hydrogen bonds : angle 4.75562 ( 381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 750 Ramachandran restraints generated. 375 Oldfield, 0 Emsley, 375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 215 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: C1 160 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7983 (ptmm) REVERT: N2 38 LYS cc_start: 0.8758 (tttm) cc_final: 0.7999 (mttp) REVERT: N2 95 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7402 (tmmt) REVERT: N2 253 GLU cc_start: 0.7873 (mm-30) cc_final: 0.6729 (pt0) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.9247 time to fit residues: 48.6913 Evaluate side-chains 48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 207 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N2 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.142557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115512 restraints weight = 12150.469| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.71 r_work: 0.3419 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3075 Z= 0.114 Angle : 0.475 4.580 4161 Z= 0.248 Chirality : 0.042 0.154 469 Planarity : 0.004 0.038 526 Dihedral : 4.052 17.313 412 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.60 % Allowed : 13.21 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.45), residues: 375 helix: 2.30 (0.61), residues: 82 sheet: 0.08 (0.41), residues: 155 loop : -1.47 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGC1 78 TYR 0.009 0.001 TYRC1 30 PHE 0.005 0.001 PHEC1 52 TRP 0.008 0.001 TRPC1 26 HIS 0.001 0.001 HISC1 88 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3072) covalent geometry : angle 0.47455 ( 4155) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.46744 ( 6) hydrogen bonds : bond 0.03231 ( 140) hydrogen bonds : angle 4.67492 ( 381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3470.27 seconds wall clock time: 59 minutes 20.56 seconds (3560.56 seconds total)